Contacts of the helix formed by residues 44 - 69 (chain F) in PDB entry 5JRE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 44 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F SER* 2.9 11.4 + - - +
42F ARG* 3.1 41.3 + - + +
43F GLU* 1.3 73.4 - - - +
45F TYR* 1.3 57.5 + - - +
46F LYS* 3.6 9.0 + - - +
47F SER* 2.7 34.9 + - - -
48F ALA* 3.0 24.4 + - - +
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Residues in contact with TYR 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F MET* 3.6 42.1 + - + -
43F GLU* 3.3 50.2 + - + +
44F ASP* 1.3 70.2 + - - +
46F LYS* 1.3 60.6 + - - +
48F ALA* 3.8 4.3 - - + -
49F ASP* 3.0 43.6 + - - +
93F ILE* 3.8 18.4 - - + +
94F LYS* 6.3 1.3 - - + -
125F LYS* 4.8 2.1 + - - -
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Residues in contact with LYS 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ASP* 3.3 7.4 + - - +
45F TYR* 1.3 78.2 - - - +
47F SER* 1.3 62.3 + - - +
49F ASP* 3.5 5.9 + - - +
50F LYS* 3.3 19.4 + - - +
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Residues in contact with SER 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F SER* 3.6 14.6 - - - -
42F ARG* 4.4 4.0 + - - -
44F ASP* 2.7 32.2 + - - -
46F LYS* 1.3 75.9 - - - +
48F ALA* 1.3 67.2 + - - +
50F LYS* 3.2 10.5 + - - +
51F TYR* 3.0 38.3 + - - -
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Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LEU* 3.2 21.9 - - + +
39F SER* 3.8 11.6 - - - -
40F MET* 3.5 35.2 - - + +
44F ASP 3.0 16.8 + - - +
45F TYR* 3.7 6.7 - - - +
46F LYS 3.3 0.2 - - - -
47F SER* 1.3 75.6 - - - +
49F ASP* 1.3 57.6 + - - +
51F TYR* 3.3 2.1 + - - -
52F LYS* 2.8 26.9 + - - +
90F TYR* 4.6 3.1 - - + -
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Residues in contact with ASP 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F TYR* 3.0 28.7 + - - +
46F LYS* 3.9 6.1 - - - +
47F SER 3.3 0.2 - - - -
48F ALA* 1.3 75.8 - - - +
50F LYS* 1.3 62.7 + - - +
52F LYS* 3.5 5.9 + - - +
53F GLU* 3.1 24.7 + - - +
90F TYR* 2.7 32.6 + - - -
94F LYS* 5.0 2.5 + - - -
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Residues in contact with LYS 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F LYS 3.3 9.8 + - - +
47F SER* 3.2 13.3 + - - +
49F ASP* 1.3 79.3 - - - +
51F TYR* 1.3 69.1 + - + +
53F GLU* 3.3 7.5 + - - +
54F GLU* 3.1 43.4 + - + +
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Residues in contact with TYR 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LYS* 4.3 11.9 + - - -
32F LEU* 3.8 23.3 - - + +
35F SER* 3.7 32.6 + - - -
36F LEU* 4.0 18.2 - - + +
39F SER* 3.3 24.9 - - - -
47F SER* 3.0 32.9 + - - +
48F ALA 3.8 3.4 - - - +
50F LYS* 1.3 82.0 - - + +
52F LYS* 1.3 57.2 + - - +
54F GLU* 3.4 14.8 + - - +
55F LEU* 2.8 32.9 + - - +
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Residues in contact with LYS 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LEU* 3.9 20.3 - - + +
48F ALA 2.8 16.5 + - - +
49F ASP* 3.8 6.3 - - - +
50F LYS 3.3 0.2 - - - -
51F TYR* 1.3 77.0 - - - +
53F GLU* 1.3 56.6 + - - +
55F LEU* 3.8 1.6 - - - +
56F THR* 2.7 46.7 + - - +
87F LEU* 3.7 22.4 - - + -
90F TYR* 3.4 40.5 + - + +
91F TYR* 3.4 26.4 + - - -
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Residues in contact with GLU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F ASP 3.1 18.3 + - - +
50F LYS* 3.6 6.6 - - - +
51F TYR 3.3 0.2 - - - -
52F LYS* 1.3 78.2 - - - +
54F GLU* 1.3 64.6 + - + +
56F THR* 3.4 4.5 + - - -
57F ASN* 3.1 42.5 + - - +
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Residues in contact with GLU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 4.0 25.7 - - + +
50F LYS* 3.1 39.3 + - + +
51F TYR* 3.8 17.5 - - - +
53F GLU* 1.3 77.8 - - + +
55F LEU* 1.3 63.1 - - - +
57F ASN* 3.3 9.8 + - - +
58F LEU* 3.0 27.1 + - + +
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F MET* 3.6 42.2 - - + +
32F LEU* 4.1 15.4 - - + +
33F SER* 3.9 26.5 - - - +
36F LEU* 4.0 10.5 - - + -
51F TYR 2.8 21.1 + - - +
52F LYS 3.8 3.4 - - - +
54F GLU* 1.3 73.2 - - - +
56F THR* 1.3 58.7 + - - +
58F LEU* 3.3 3.1 + - - +
59F ALA* 2.9 30.1 + - - +
83F TYR* 3.8 21.8 - - + -
86F ALA* 4.2 3.4 - - + -
87F LEU* 3.7 23.8 - - + -
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Residues in contact with THR 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F LYS* 2.7 36.4 + - - +
53F GLU* 3.8 5.6 - - - -
55F LEU* 1.3 76.8 - - - +
57F ASN* 1.3 61.4 + - - +
59F ALA* 3.3 2.3 + - - +
60F LYS* 3.0 38.1 + - + +
83F TYR* 4.1 26.2 - - - +
87F LEU* 4.5 6.9 - - - +
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Residues in contact with ASN 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F GLU* 3.1 37.8 + - - +
54F GLU* 3.6 7.6 - - - +
56F THR* 1.3 76.2 - - - +
58F LEU* 1.3 66.9 + - + +
60F LYS* 3.3 9.5 + - - +
61F THR* 3.2 24.9 + - - -
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Residues in contact with LEU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F ARG* 3.7 13.9 - - + +
28F ARG* 3.9 48.5 - - + +
29F MET* 3.8 22.2 - - + -
32F LEU* 3.7 26.0 - - + -
54F GLU* 3.0 15.3 + - + +
55F LEU 3.7 7.2 - - - +
57F ASN* 1.3 75.9 - - + +
59F ALA* 1.3 57.8 + - - +
61F THR* 3.2 8.2 + - - +
62F GLN* 2.8 29.8 + - - +
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Residues in contact with ALA 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F MET* 3.7 19.5 - - + +
55F LEU 2.9 17.2 + - - +
56F THR 3.5 5.2 - - - +
58F LEU* 1.3 76.0 - - - +
60F LYS* 1.3 58.4 + - - +
62F GLN* 3.3 1.9 + - - +
63F ILE* 2.8 37.7 + - + +
80F LEU* 4.3 2.0 - - + -
83F TYR* 3.6 39.9 - - + +
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Residues in contact with LYS 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F THR* 3.0 23.7 + - + +
57F ASN* 3.5 11.9 - - - +
58F LEU 3.3 0.2 - - - -
59F ALA* 1.3 76.7 - - + +
61F THR* 1.3 61.5 + - - +
63F ILE* 3.5 9.9 + - + +
64F GLU* 3.2 22.9 + - - +
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Residues in contact with THR 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F ARG* 3.8 28.9 - - - +
57F ASN 3.2 13.0 + - - -
58F LEU* 3.6 11.3 - - - +
60F LYS* 1.3 76.1 - - - +
62F GLN* 1.3 63.6 + - - +
64F GLU* 2.9 33.9 - - + +
65F GLU* 3.0 14.7 + - + +
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Residues in contact with GLN 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ILE* 3.1 45.9 + - - +
25F ARG* 2.8 40.1 + - - +
26F SER* 3.5 16.0 - - - +
29F MET* 3.9 14.9 - - - -
58F LEU 2.8 20.1 + - - +
59F ALA* 3.7 4.0 - - - +
61F THR* 1.3 73.5 - - - +
63F ILE* 1.3 63.7 + - - +
65F GLU* 3.2 1.3 + - - +
66F LEU* 2.9 34.8 + - + +
76F GLY* 3.9 12.2 + - - +
80F LEU* 4.3 19.3 - - + -
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Residues in contact with ILE 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ALA* 2.8 30.4 + - + +
60F LYS* 3.8 9.4 - - + +
62F GLN* 1.3 77.5 - - - +
64F GLU* 1.3 62.7 + - - +
66F LEU* 3.5 4.8 + - - +
67F LYS* 3.2 45.8 + - + +
80F LEU* 3.8 22.2 - - + -
104F LEU 4.3 6.1 - - - +
105F GLY* 3.5 29.6 - - - +
106F VAL* 4.0 17.7 - - + -
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Residues in contact with GLU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F LYS 3.2 13.1 + - - +
61F THR* 2.9 32.2 - - - +
63F ILE* 1.3 79.1 - - - +
65F GLU* 1.3 80.4 + - - +
67F LYS* 3.5 13.6 + - + +
68F LYS* 3.3 42.7 + - - +
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Residues in contact with GLU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F LYS* 3.3 35.1 - - - +
21F GLU* 4.4 5.0 - - - +
22F ILE* 4.4 13.2 - - + +
25F ARG* 3.8 26.1 + - - +
61F THR* 3.0 27.1 + - + +
62F GLN 3.2 3.8 + - - +
64F GLU* 1.3 93.1 - - - +
66F LEU* 1.3 61.8 + - - +
68F LYS* 3.2 17.9 + - - +
69F TYR* 3.0 39.9 + - - +
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Residues in contact with LEU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E PRO* 5.3 3.8 - - - +
22F ILE* 3.8 27.6 - - + -
62F GLN* 2.9 21.4 + - + +
63F ILE* 4.0 3.8 - - - +
65F GLU* 1.3 73.3 - - - +
67F LYS* 1.3 65.1 + - + +
69F TYR 3.3 3.7 - - - -
70F PRO* 3.2 26.9 - - - +
72F PHE 3.5 27.6 - - - +
73F TYR* 3.8 40.2 - - + +
76F GLY* 4.3 8.1 - - - -
77F PHE 4.9 0.2 - - - +
80F LEU* 3.6 30.7 - - + -
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Residues in contact with LYS 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E PRO* 6.2 5.6 - - + -
63F ILE* 3.2 35.8 + - + +
64F GLU* 3.5 15.7 - - - +
65F GLU 3.2 0.2 - - - -
66F LEU* 1.3 79.6 - - - +
68F LYS* 1.3 62.3 + - + +
70F PRO* 3.6 10.4 - - - +
105F GLY 5.2 2.6 + - - -
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Residues in contact with LYS 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F GLU* 3.3 33.7 + - - +
65F GLU* 3.2 23.3 + - - +
67F LYS* 1.3 77.3 - - + +
69F TYR* 1.3 87.7 + - + +
70F PRO* 3.4 6.8 - - - +
71F MET* 5.2 0.7 - - - +
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Residues in contact with TYR 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LYS* 2.8 32.5 + - - -
15F LEU* 3.6 26.9 - - + -
18F LYS* 3.5 47.9 - - + -
22F ILE* 4.4 7.1 - - + +
65F GLU* 3.0 33.3 + - - +
66F LEU* 3.3 8.3 - - - +
68F LYS* 1.3 104.1 - - + +
70F PRO* 1.3 60.1 - - - +
71F MET* 3.1 9.4 - - + -
72F PHE* 2.9 39.9 + - + +
73F TYR 3.9 1.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il